Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations

The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus’ range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.

Supplementary Figure 2. Admixture proportions of the blue wildebeest.Ancestry proportions of the blue wildebeest were inferred by ADMIXTURE with the assumed number of ancestry (K) ranging from 2 to 11.First degree relatives and duplicates were excluded prior to the analysis.Sites with minor allele frequency (MAF) lower than 0.05 and high linkage disequilibrium (LD, r 2 > 0.7) were omitted from the analysis.ADMIXTURE analysis was conducted based on 0.9 million SNPs, which were randomly selected from the filtered sites.Supplementary Figure 9. Admixture proportions of the black and blue wildebeest for all 131 samples.Ancestry proportions of the black and blue wildebeest were inferred by the ADMIXTURE with assumed number of ancestry (K) ranging from 2 to 13.We used the imputed dataset and filtered out sites with high LD (r 2 > 0.6).We then randomly selected one million SNPs for the ADMIXTURE analysis.Individuals were ordered by their estimated ancestry proportions at each K. expected for a population composed of individuals of high genetic uniformity, LD curves plateau and stabilize to a constant value with a few Mb for all the nine blue wildebeest populations.However, the black wildebeest population plateaued at a higher value, which was likely driven by the severe bottleneck experienced in the 1900s.Non-homogenous populations of blue wildebeest-B-Ovita and B-Zimbabwe, exhibited similar patterns as the black wildebeest, suggesting possible substructure within them (Fig. S6).
The final selection of homogenous populations includes only individuals sequenced on the MGI platform.Although we did not see any indication of batch bias, this selection of individuals also rules out the possibility of batch bias caused by the sequencing platform.
wildebeest [12][13][14] .Our samples from this area were collected between 1992-1995, and in our data this population still retains the genetic features characteristic of a migratory wildebeest population, such as higher heterozygosity, fewer ROHs and long-distance genetic connectivity.Similarly, also the brindled wildebeest population in Etosha was a migratory population until recently, but encompassing a smaller geographical range than the two examples above 4 .This population also clearly shows the genetic migration syndrome.
It was not within the scope of our study to perform a detailed classification of blue wildebeest populations along this continuum.Instead, we have defined populations that inhabit the two areas of the blue wildebeest range where all sources agree on the existence of long-distance wildebeest migrations until circa 1960 as 'migratory', and all other populations as 'non-migratory'.Our genetic results showing the presence of a 'migration syndrome' suggest that such a distinction, while a simplification of a more complex range of migratory conditions, indeed has some merit.
In the following we quote excerpts from Estes & East (2009) 3 that support our definitions of current and former migratory populations of blue wildebeest (our emphasis in bold):

Eastern white bearded (p. 72)
Like the gnu populations of the northern Kalahari region, to which the Masai steppe is comparable, the main population of eastern Masailand was nomadic and migratory.There were also several small satellite populations with sedentary habits in areas with permanent water.In pre-colonial days, the open grassland and Acacia savanna which covered virtually the whole of Masailand formed the wet-season dispersal area for wildebeest, zebra, and Thomson's gazelle, the three most numerous and most migratory plains species.[...] The amount of game that inhabited eastern Masailand in former times is unknown.Considering that the Serengeti region currently carries over a million head of large mammals, the far larger area of eastern Masailand could presumably have carried at least as many.Surely the gnu population must have numbered at least 100,000 at the end of the 19th century.

Eastern white bearded (p. 95)
The eastern white-bearded wildebeest formerly ranged widely over the open grasslands and acacia savannas of the Masai steppe in northern Tanzania, to the east of the Gregory Rift Valley.At the end of the 19th century, virtually the whole of eastern Masailand was probably a wetseason dispersal area for migratory plains game, which concentrated around permanent sources of water during the dry season; though numbers are unknown, there were probably at least hundreds of thousands of wildebeest.

Kalahari population (pp89-90)
The Kalahari Desert, which occupies most of Botswana, the northern Cape of South Africa, and eastern Namibia, formerly supported one of Africa's great plains-game ecosystems.[...] During the wet season, a large migratory wildebeest population dispersed throughout the Kalahari savannas.When these areas became waterless for several months during the dry season, and especially in severe drought years, the wildebeest concentrated near permanent water in areas such as the Makgadikgadi Pans, the Lake Ngami depression and the Chobe River in Botswana, the floodplains bordering the Okavango Swamp in Botswana and Namibia, Etosha Pan, Ovamboland and the Caprivi Strip in Namibia, along the Cunene and Cubango Rivers in Angola, and formerly along the Limpopo River in Botswana and South Africa, and the Orange River in South Africa.This vast region may have been occupied by a single wildebeest population, which dispersed widely during the wet season but broke up into separate concentrations during the dry season.Its size will never be known, but it must have comprised at least several hundred thousand individuals.

Supplementary Figure 26 .
Genotype calls, proportions of heterozygous sites and SNP density for ROH validation in an Eastern white-bearded wildebeest sample (CTauKeS__716).For each chromosome, blue vertical bars indicate homozygous sites, and red vertical bars are superimposed to show heterozygous sites.Identified ROHs are marked by black horizontal bars.The gray line below homozygous/heterozygous calls shows proportions of heterozygous calls in a window of 100 kb.The purple line below shows the number of SNPs along the 100 kb window.Supplementary Figure 27.Genotype calls, proportions of heterozygous sites and SNP density for ROH validation in a Western white-bearded wildebeest sample (CTauKeW__649).For each chromosome, blue vertical bars indicate homozygous sites, and red vertical bars are superimposed to show heterozygous sites.Identified ROHs are marked by black horizontal bars.The gray line below homozygous/heterozygous calls shows proportions of heterozygous calls in a window of 100 kb.The purple line below shows the number of SNPs along the 100 kb wind